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Magnesium in PDB 3dxj: Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin

Enzymatic activity of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin, PDB code: 3dxj was solved by K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 235.090, 235.090, 250.880, 90.00, 90.00, 120.00
R / Rfree (%) 23.5 / 28.9

Other elements in 3dxj:

The structure of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin (pdb code 3dxj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin, PDB code: 3dxj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3dxj

Go back to Magnesium Binding Sites List in 3dxj
Magnesium binding site 1 out of 3 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:56.0
occ:1.00
OD2 B:ASP168 2.4 77.7 1.0
O D:LYS840 2.5 65.6 1.0
O D:HOH1531 2.8 11.3 1.0
OE2 B:GLU154 3.0 88.3 1.0
CG B:ASP168 3.1 75.6 1.0
OD1 B:ASP168 3.1 70.0 1.0
C D:LYS840 3.5 66.6 1.0
CA D:TYR841 3.6 65.4 1.0
N D:VAL842 3.7 64.4 1.0
CG2 D:VAL842 3.8 68.5 1.0
N D:TYR841 4.0 66.0 1.0
CD B:GLU154 4.2 90.3 1.0
C D:TYR841 4.2 64.1 1.0
NZ B:LYS83 4.5 83.5 1.0
CB B:ASP168 4.5 77.2 1.0
OE1 B:GLU154 4.6 89.2 1.0
O D:LEU839 4.6 73.4 1.0
O D:VAL842 4.7 65.5 1.0
CA D:LYS840 4.7 68.0 1.0
CB D:TYR841 4.8 66.3 1.0
CA D:VAL842 4.8 65.1 1.0
CB D:VAL842 4.8 66.5 1.0
CD2 D:TYR841 4.9 76.6 1.0

Magnesium binding site 2 out of 3 in 3dxj

Go back to Magnesium Binding Sites List in 3dxj
Magnesium binding site 2 out of 3 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1527

b:79.5
occ:1.00
O D:HOH1530 2.5 23.4 1.0
OD2 D:ASP743 2.6 70.3 1.0
OD1 D:ASP739 2.6 75.2 1.0
OD1 D:ASP741 2.8 69.3 1.0
OD2 D:ASP741 2.9 71.7 1.0
OD1 D:ASP743 3.0 71.7 1.0
CG D:ASP743 3.0 69.5 1.0
CG D:ASP741 3.2 69.4 1.0
CG D:ASP739 3.7 71.6 1.0
NH2 D:ARG704 3.8 77.8 1.0
OD2 D:ASP739 4.1 72.9 1.0
O D:ASP739 4.2 55.8 1.0
N D:ASP739 4.3 61.0 1.0
CB D:ASP743 4.4 63.6 1.0
N D:ASP743 4.6 59.3 1.0
CB D:ASP741 4.7 64.4 1.0
CA D:ASP743 4.9 59.5 1.0
C D:ASP739 4.9 57.3 1.0
CB D:ASP739 4.9 65.3 1.0
CA D:ASP739 5.0 59.8 1.0

Magnesium binding site 3 out of 3 in 3dxj

Go back to Magnesium Binding Sites List in 3dxj
Magnesium binding site 3 out of 3 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg1527

b:56.9
occ:1.00
OD2 N:ASP743 2.4 68.5 1.0
OD1 N:ASP741 2.4 69.3 1.0
OD1 N:ASP743 2.5 70.2 1.0
OD1 N:ASP739 2.6 61.4 1.0
OD2 N:ASP741 2.6 65.7 1.0
CG N:ASP743 2.7 66.8 1.0
CG N:ASP741 2.8 66.3 1.0
O N:HOH1529 2.9 30.3 1.0
CG N:ASP739 3.7 58.8 1.0
NH2 N:ARG704 3.9 66.1 1.0
CB N:ASP743 4.1 62.0 1.0
OD2 N:ASP739 4.1 59.6 1.0
CB N:ASP741 4.3 61.0 1.0
N N:ASP743 4.4 57.2 1.0
O N:ASP739 4.5 55.3 1.0
N N:ASP739 4.5 59.5 1.0
CA N:ASP743 4.6 60.2 1.0
N N:ASP741 4.8 56.6 1.0
N N:GLY742 4.9 54.7 1.0
C N:ASP739 4.9 55.0 1.0
CB N:ASP739 4.9 58.2 1.0

Reference:

J.Mukhopadhyay, K.Das, S.Ismail, D.Koppstein, M.Jang, B.Hudson, S.Sarafianos, S.Tuske, J.Patel, R.Jansen, H.Irschik, E.Arnold, R.H.Ebright. The Rna Polymerase "Switch Region" Is A Target For Inhibitors. Cell(Cambridge,Mass.) V. 135 295 2008.
ISSN: ISSN 0092-8674
PubMed: 18957204
DOI: 10.1016/J.CELL.2008.09.033
Page generated: Wed Aug 14 12:44:48 2024

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